Category Archives: News

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HuPro44_2

Huygens Professional

Our image processing workstation is now equipped with Huygens Professional (desktop). Compared to our Huygens Remote Manager (HRM) the HuPro allows for more flexibility and provides some additional functionality.

The new HuPro desktop version of the Huygens software is intended to accelerate the optimization of the deconvolution parameter and do advanced image restoration using measured point spread functions (in contrast to the theoretical PSF).

This new license replaces the Huygens Essential that was previously accessible via remote desktop connection.

imaris-filament-example

Imaris 9.3

Imaris 9.3 is available. Find out more about the software on the Bitplane website.

The first apparent change will be the end of the arena. Instead of its own database, there is now the possibility to add ‘observed’ folders to Imaris to facilitate the access to your ims-files.
The first time Imaris is launched, you will be prompted to use the migration assistant, that allows to extract existing images from the arena. You can find a short tutorial in this video.

You might also wonder look in vain for functionality like filtering or background subtraction under  Menu > Image Processing. Now instead there is a new icon in the toolbar:

imaris-ip-icon

This will bring up the following window where you can chain together all the basic pre-processing operations together for the different channels of your dataset.

imaris-ip-window

The complete list of novelties can be found on the ‘what’s new‘ page. You might also be interested in the change-list in the release notes.

We installed this latest version on our number crunchers.

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FPbase

fpbase.org is a beautiful web-application to browse the contents of the Fluorescent Protein Database. There is a lot of linked content such as excitation and emission spectra or the publications reporting on the molecules. Check it out!

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Demo: Leia SP8 FALCON

leica_dmi8

At the beginning of this year we will continue the demo series for the laser scanning confocal system. Leica will bring their SP8 FALCON system for a week.

Dates: 11-20 January 2019
Location: PER017, 013

Key Features

  • Inverted microscope (DMi8)
  • Fully motorised
  • White Light Laser (WLL)
  • Acousto-Optical Beam-Splitter (AOBS) 470-670
  • 405 Diode
  • Hybrid detectors HyD
  • FLIM module FALCON
  • Simultaneous multiple colors and super-resolution mode LIGHNING
  • Stage application module NAVIGATOR

 

Objectives

FLATFIELD CORRECTION Chromatic CORRECTION MAG. NA IMMERSION Remarks
Plan FLUOTAR 4 0.13 Dry
Plan Apochromat 10 0.45 Dry CS2
Plan Apochromat 20 0.75 Dry CS2
Plan Apochromat 40 1.10 Water CS2 motCORR
Plan Apochromat 63 1.4 Oil CS2
Plan Apochromat 63 1.3 Glyc. CORR CS2

Schedule

dates description
14.-15. Jan. Installation of the system
16.-17 Jan. Demo by Nathalie Garin.
People with samples can reserve 1 hour slots.
For 1 hour demos without your own samples, please organise in groups of 1-4 people.
18. Jan. Further testing (reserve)
21. Jan. Dismounting of the system

 

Demo-Slot Booking

To reserve a slot for the demo please login.

imaris-track-example

Imaris Workshop 11. September 2018

At the University of Fribourg we use Imaris to process and analyse multidimensional image data-sets issue from epi-fluorescene microscopy.  In particular we use it’s advanced functionality for 3 dimensional (optically sectioned) image data and perform volumetric analysis.

We organise a worksop with representatives of Bitplane for you, to discover the possibilities of the software and train yourself as a user.

Further information:

Organisation

date: 11. September 2018 from 9:00-17:00
location: PER II, F230
participation conditions: UniFr staff, free of charge, registration required

Participants are free to only attend the presentation of Imaris or to work through the entire workshop.

Schedule

TIME DESCRIPTION
 09:00-10:30 presentation of Imaris (functionality, use cases)
 10:30-10:45   coffee break
 11:00-13:00 introduction to Imaris (basics)
13:00-14:00   lunch break
14:00-15:30 hands-on workshop
15:30-16:00   coffee break
16:00-17:30 hands-on workshop

 

Registration

registration closed.

scijava-notebook_nuclei-counting

Bioimage-Informatics Clinic

In 2018, effective immediately, we like to introduce the Bioimage-Informatic-Clinic.

This means that once a week our door is open for you to seek council for image and data analysis and general topics around microscopy data. Topics include: image restoration, deconvolution, volume reconstruction, image alignment (registration), 3D image processing, object segmentation, object tracking, object quantification, co-localisation analysis, batch processing, data visualisation, data analysis pipelines, data management and many more.

Every Tuesday afternoon from 13:00 – 17:00  you can bring your microscopy data (external HD or the server address) and your questions  to PER02 1.406.
Visitors will be attended to on a first come first served basis (no need to arrange a meeting). Come around, hang-out and let’s crunch some numbers.

threadripper

New Image Analysis Workstation

For those who spent a lot of time waiting for the computer to finish some image analysis task, we acquired a new desktop computer that might help remedy this loss of time. This new computer has a hardware configuration for large datasets that require computationally intensive processing.
You can find more details on number cruncher’s page. This workstation is henceforth available for all facility users.

omero_fpbioimage_screenshot

OMERO update

We updated our OMERO.server from 3.3.1 to 3.3.5

During the upgrade we optimized the server’s software dependencies for optimal performance.

In case your desktop clients do not connection to the server anymore, please update the OMERO.insight on you computer too. You find instruction and the download of the pre-configured clients on our web-site.

omero 5.3.5 upgrade

There is also a new goodie: FPBioimage is a 3D viewer for the web. It is currently in beta, so some irregularities are expexted. Also you should make sure you have a fast internet connection.

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